ArticleJournal of chemical information and modeling2019
Conformation and Permeability: Cyclic Hexapeptide Diastereomers.
Article in Journal of chemical information and modeling, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
31 citing papers in PubMed, 66 citations in OpenAlex.
- Article
- Exploring Passive Permeability Profiles of Cyclic Heptapeptide Chemical Space Uncovers Bioactivity of Mortiamide Scaffold Driven by Colloidal Aggregation.Chembiochem : a European journal of chemical biology · 2026Article
- Bridging Heterocycle-Mediated Hydrogen Bonding Facilitates Permeability of Polar Macrobicycles.Journal of the American Chemical Society · 2026Article
- Permeation enhancer-induced membrane defects assist the oral absorption of peptide drugs.Nature communications · 2025Article
- MultiCycPermea: accurate and interpretable prediction of cyclic peptide permeability using a multimodal image-sequence model.BMC biology · 2025Article
- Validating Small-Molecule Force Fields for Macrocyclic Compounds Using NMR Data in Different Solvents.Journal of chemical information and modeling · 2024Article
- CycPeptMP: enhancing membrane permeability prediction of cyclic peptides with multi-level molecular features and data augmentation.Briefings in bioinformatics · 2024Article
- Membrane Permeability in a Large Macrocyclic Peptide Driven by a Saddle-Shaped Conformation.Journal of the American Chemical Society · 2024Article
- Gaussian accelerated molecular dynamics simulations facilitate prediction of the permeability of cyclic peptides.PloS one · 2024Article
- Molecular chameleons in drug discovery.Nature reviews. Chemistry · 2024Review
- Oral Absorption of Middle-to-Large Molecules and Its Improvement, with a Focus on New Modality Drugs.Pharmaceutics · 2023Review
- Targeted Protein Degradation: Advances, Challenges, and Prospects for Computational Methods.Journal of chemical information and modeling · 2023Review
- Mixture-Based Screening of Focused Combinatorial Libraries by NMR: Application to the Antiapoptotic Protein hMcl-1.Journal of medicinal chemistry · 2023Article
- Training Neural Network Models Using Molecular Dynamics Simulation Results to Efficiently Predict Cyclic Hexapeptide Structural Ensembles.Journal of chemical theory and computation · 2023Article
- CycPeptMPDB: A Comprehensive Database of Membrane Permeability of Cyclic Peptides.Journal of chemical information and modeling · 2023Article
- Amide-to-ester substitution as a stable alternative to N-methylation for increasing membrane permeability in cyclic peptides.Nature communications · 2023Article
- Natural Lipid Extracts as an Artificial Membrane for Drug Permeability Assay: In Vitro and In Silico Characterization.Pharmaceutics · 2023Article
- Lessons for Oral Bioavailability: How Conformationally Flexible Cyclic Peptides Enter and Cross Lipid Membranes.Journal of medicinal chemistry · 2023Article
- Lipid Composition Is Critical for Accurate Membrane Permeability Prediction of Cyclic Peptides by Molecular Dynamics Simulations.Journal of chemical information and modeling · 2022Article
- A New Amino Acid for Improving Permeability and Solubility in Macrocyclic Peptides through Side Chain-to-Backbone Hydrogen Bonding.Journal of medicinal chemistry · 2022Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
Abstract
Conformational ensembles of eight cyclic hexapeptide diastereomers in explicit cyclohexane, chloroform, and water were analyzed by multicanonical molecular dynamics (McMD) simulations. Free-energy landscapes (FELs) for each compound and solvent were obtained from the molecular shapes and principal component analysis at T = 300 K; detailed analysis of the conformational ensembles and flexibility of the FELs revealed that permeable compounds have different structural profiles even for a single stereoisomeric change. The average solvent-accessible surface area (SASA) in cyclohexane showed excellent correlation with the cell permeability, whereas this correlation was weaker in chloroform. The average SASA in water correlated with the aqueous solubility. The average polar surface area did not correlate with cell permeability in these solvents. A possible strategy for designing permeable cyclic peptides from FELs obtained from McMD simulations is proposed.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.